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RNA Seq HTSeq download GDC portal

Hi friends,

I am trying to download ht-seq file form GDC portal but it gives me one file for each patients. Can you please let me know how to download one file including all patients together for all 60000 genes?

Is there any R code for this?

Thank you

rna-seq gdc-portal
• 2,208 views • link
updated by Zhenyu Zhang Zhenyu Zhang • written by Rob • Rob

Btw, HTSeq workflow is no longer supported in the GDC. You probably want to transit to STAR Count now

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written by Zhenyu Zhang Zhenyu Zhang

2 answers

You can use:

xenabrowser

or

r package TCGAbiolinks

• 0 views • link
written by DareDevil DareDevil

Thank you dare_devil

• 0 views • link
written by Rob • Rob

Whatever method you tried, internally it stills need to download all files, before the RNA API is in production.

There are some R tools doing that, or you can use "GDC RNA tool" listed here https://gdc.cancer.gov/access-data/gdc-community-tools for aggregation

• 0 views • link
written by Zhenyu Zhang Zhenyu Zhang

thanks Zhenyu Zhang

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written by Rob • Rob

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